suppressPackageStartupMessages({
library(tidyverse)
library(plotly)
library(treeio)
library(ggtree)
library(ggtreeExtra)
library(svglite)
})
BGC table for Myxococcota
Rscript notebook/bgc_table.R \
--antismash_dir ~/p__Nitrospirota_all/antismash/6.0.1/ \
--bigscape_dir ~/p__Nitrospirota_all/p__Nitrospirota_all_antismash_6.0.1/network_files/2022-02-01_16-12-56_glocal_p__Nitrospirota_all_antismash_6.0.1/ \
--output tables/p__Nitrospirota_all_bgcs.csv
## # A tibble: 7,699 × 9
## bgc_id GCF genome_id contig start end product contig_edge class
## <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <lgl> <chr>
## 1 BBCX01000006.… 0;28… GCA_0013… BBCX0… 103791 119963 betala… TRUE Othe…
## 2 BDSY01000037.… 2327 GCA_0028… BDSY0… 18239 39643 ranthi… FALSE RiPPs
## 3 BDSY01000065.… 2326 GCA_0028… BDSY0… 0 18215 ranthi… TRUE RiPPs
## 4 BDSZ01000026.… 13 GCA_0028… BDSZ0… 8603 49803 ladder… FALSE Othe…
## 5 BDSZ01000032.… 14 GCA_0028… BDSZ0… 1097 43731 NRPS-l… FALSE NRPS
## 6 BDSZ01000042.… 5 GCA_0028… BDSZ0… 0 20604 ladder… TRUE Othe…
## 7 BDTA01000096.… 16 GCA_0028… BDTA0… 18335 39755 ranthi… FALSE RiPPs
## 8 BDTA01000122.… 15 GCA_0028… BDTA0… 47296 70788 ladder… TRUE Othe…
## 9 BDTB01000167.… 8;23… GCA_0028… BDTB0… 0 7268 ladder… TRUE Othe…
## 10 BDTC01000008.… 9 GCA_0028… BDTC0… 0 21965 NRPS;T… TRUE PKS-…
## # … with 7,689 more rows
Genome table for Myxococcota
## # A tibble: 317 × 11
## genome_id total_bgcs bgcs_on_contig_edge gtdb_taxonomy assembly_level
## <chr> <dbl> <dbl> <chr> <chr>
## 1 GCA_016706135.1 9 1 d__Bacteria;p_… Contig/Scaffo…
## 2 GCA_016709365.1 10 0 d__Bacteria;p_… Contig/Scaffo…
## 3 GCA_016712165.1 10 0 d__Bacteria;p_… Contig/Scaffo…
## 4 GCA_016711755.1 9 1 d__Bacteria;p_… Contig/Scaffo…
## 5 GCA_016715825.1 9 0 d__Bacteria;p_… Contig/Scaffo…
## 6 GCA_016719745.1 10 0 d__Bacteria;p_… Contig/Scaffo…
## 7 GCA_016722315.1 10 0 d__Bacteria;p_… Contig/Scaffo…
## 8 GCA_016722055.1 11 0 d__Bacteria;p_… Contig/Scaffo…
## 9 GCA_001567445.1 11 7 d__Bacteria;p_… Contig/Scaffo…
## 10 GCA_001805205.1 2 2 d__Bacteria;p_… Contig/Scaffo…
## # … with 307 more rows, and 6 more variables: checkm_completeness <dbl>,
## # checkm_contamination <dbl>, genome_size <dbl>, ncbi_bioproject <chr>,
## # mimag_quality <chr>, source <chr>
Customize BiG-SCAPE classes and color palette
bigscape_classes <- c("Terpene",
"RiPPs",
"NRPS",
"PKS-NRP_Hybrids",
"PKSI",
"PKSother",
"Saccharides",
"Others")
my_classes <- c("Terpene",
"RiPP",
"NRPS",
"NRPS-PKS",
"PKS",
"PKS",
"Other",
"Other")
my_colors <- c("#ff8800",
"#20c200",
"#ff0000",
"#dd00ff",
"#0d00ff",
"#757575")
QC Boxplots for the phylum Nitrospirota
Overview of the phylum Myxococcota. Add number of MAGs per clade
Absence / Presence matrix for f__Nitrospiraceae